Pocket Guide to Clinical Microbiology. Christopher D. Doern
ActinomycetaceaeGenus. ActinobaculumGenus. ActinomycesGenus. ArcanobacteriumGenus. MobiluncusGenus. TrueperellaFamily. CorynebacteriaceaeGenus. CorynebacteriumGenus. TuricellaFamily. DietziaceaeGenus. DietziaFamily. MycobacteriaceaeGenus. MycobacteriumFamily. NocardiaceaeGenus. GordoniaGenus. NocardiaGenus. RhodococcusFamily. TsukamurellaceaeGenus. TsukamurellaFamily. PropionibacteriaceaeGenus. PropionibacteriumFamily. StreptocmycetaceaeGenus. StreptomycesFamily. NocardiopsaceaeGenus. NocardiopsisFamily. BifidobacteriaceaeGenus. AlloscardoviaGenus. BifidobacteriumGenus. GardnerellaFamily. BrevibacteriaceaeGenus. BrevibacteriumFamily. CellulomonadaceaeGenus. CellulomonasGenus. OerskoviaGenus. TropherymaFamily. DermabacteraceaeGenus. DermabacterGenus. HelcobacillusFamily. DermacoccaceaeGenus. DermacocccusGenus. KytococcusFamily. MicrobacteriaceaeGenus. LeifsoniaGenus. MicrobacteriumFamily. MicrococcaceaeGenus. ArthrobacterGenus. KocuriaGenus. MicrococcusGenus. RothiaGenus. StomatococcusClass. CoriobacteriiaFamily. AtopobiaceaeGenus. AtopobiumFamily. EggerthellaceaeGenus. EggerthellaGenus. SlackiaClass. BacteroidiaFamily. BacteroidaceaeGenus. BacteroidesFamily. PorphyromonadaceaeGenus. DysgonomonasGenus. MicrobacterGenus. ParabacteroidesGenus. PorphyromonasGenus. TannerellaFamily. PrevotellaceaeGenus. PrevotellaClass. FlavobacteriiaFamily. FlavobacteriaceaeGenus. BergeyellaGenus. CapnocytophagaGenus. ChryseobacteriumGenus. ElizabethkingiaGenus. EmpedobacterGenus. FlavobacteriumGenus. WeeksellaClass. SphingobacteriiaFamily. SphingobacteriaceaeGenus. SphingobacteriumClass. ChlamydiaeFamily. ChlamydiaceaeGenus. ChlamydiaGenus. ChlamydophilaClass. Bacilli or FibribacteriaFamily. BacillaceaeGenus. BacillusFamily. ListeriaceaeGenus. ListeriaFamily. PaenibacillaceaeGenus. PaenibacillusFamily. StaphylococcaceaeGenus. StaphylococcusFamily. Unassigned Genus.GemellaFamily. AerococcaceaeGenus. AbiotrophiaGenus. AerococcusGenus. DolosicoccusGenus. FacklamiaGenus. GlobicatellaFamily. CarnobactericeaeGenus. AlloiococcusGenus. DolosigranulumGenus. GranulicatellaFamily. EnterococcaceaeGenus. EnterococcusGenus. VagococcusFamily. LactobacillaceaeGenus. LactobacillusGenus. PediococcusFamily. LeuconostocaceaeGenus. LeuconostocGenus. WeissellaFamily. StreptococcaceaeGenus. LactococcusGenus. StreptococcusClass. ClostridiaFamily. ClostridiaceaeGenus. ClostridiumGenus. SarciniaFamily. PeptococcaceaeGenus. PeptococcusFamily. PeptostreptococcaceaeGenus. PeptostreptococcusFamily. UnassignedGenus. AnaerococcusGenus. FinegoldiaGenus. HelcococcusGenus. PeptoniphilusClass. ErysipelotrichiaFamily. ErysipelotrichaceaeGenus. ErysipelothrixClass. NegativicutesFamily. VeillonellaceaeGenus. VeillonellaClass. FusobacteriiaFamily. FusobacteriaceaeGenus. FusobacteriumFamily. LeptotrichiaceaeGenus. LeptotrichiaGenus. SneathiaGenus. StreptobacillusClass. AlphaproteobcteriaFamily. CaulobacteraceaeGenus. BrevundimonasFamily. BartonellaceaeGenus. BartonellaFamily. BrucellaceaeGenus. BrucellaGenus. OchrabactrumFamily. RhizobiaceaeGenus. AgrobacteriumGenus. RhizobiumFamily. RhodobacteraceaeGenus. ParacoccusFamily. AcetobacteraceaeGenus. RoseomonasFamily. RhodospirllaceaeGenus. InquilinusFamily. AnaplasmataceaeGenus. AnaplasmaGenus. EhrlichiaGenus. WolbachiaFamily. RickettsiaceaeGenus. OrientiaGenus. RickettsiaFamily. SphingomonadaceaeGenus. SphingomonasClass. BetaproteobacteriaFamily. AlcaligenaceaeGenus. AchoromobacterGenus. AlcaligenesGenus. BordetellaGenus. OligellaFamily. BurkholderiaceaeGenus. BurkholderiaGenus. CupriavidisGenus. PandoraeaGenus. RalstoniaFamily. ComamonadaceaeGenus. AcidovoraxGenus. ComamonasGenus. DefltiaFamily. OxalobacteraceaeGenus. HerbaspirillumFamily. NeisseriaceaeGenus. EikenellaGenus. KingellaGenus. NeisseriaFamily. SprillaceaeGenus. Genera Genus. SprilliumClass. EpsilonproteobacteriaFamily. CampylobacteraceaeGenus. ArcobacterGenus. CampylobacterFamily. HelicobacteraceaeGenus. HelicobacterClass. GammaproteobacteriaFamily. EnterobacteriaceaeGenus. CedeceaGenus. CitrobacterGenus. CronobacterGenus. EdwardsiellaGenus. EnterobacterGenus. ErwiniaGenus. EscherichiaGenus. HafniaGenus. KlebsiellaGenus. KluyberaGenus. LeclerciaGenus. MorganellaGenus. PantoeaGenus. PlesiomonasGenus. ProteusGenus. ProvidenciaGenus. RaoltellaGenus. SalmonellaGenus. SerratiaGenus. ShigellaGenus. YersiniaGenus. YokenellaFamily. VibrionaceaeGenus. VibrioFamily. AeromonadaceaeGenus. AeromonasFamily. ShewanellaceaeGenus. ShewanellaFamily. CardiobacteriaceaeGenus. CardiobacteriumGenus. SuttonellaFamily. CoxiellaceaeGenus. CoxiellaFamily. LegionellaceaeGenus. LegionellaFamily. PasteurellaceaeGenus. ActinobacillusGenus. AggregatibacterGenus. HaemophilusGenus. PasteurellaFamily. MoraxelaceaeGenus. AcinetobacterGenus. BranhamellaGenus. MoraxellaFamily. PseudomonadaceaeGenus. ChryseomonasGenus. FlavimonasGenus. PseudomonasFamily. FrancisellaceaeGenus. FrancisellaClass. SpirochaetesFamily. BrachyspiraceaeGenus. BrachyspiraFamily. LeptospiraceaeGenus. LeptospiraFamily. BorreliaceaeGenus. BorreliaFamily. SpirochaetaceaeGenus. TreponemaClass. MollicutesFamily. MycoplasmataceaeGenus. MycoplasmaGenus. Ureaplasma
Taxonomic Classification of Human Viruses
The taxonomy of viral classification is arranged in the following way…
OrderFamilySubfamilyGenusSpecies
Practically speaking, most clinical microbiologists organize viruses in terms of genome structure, family, and genus, and only rarely are the subfamily or species designations utilized. As such, the following taxonomic structure is presented in terms of what would be most useful to the practicing clinical microbiologist.
Single-stranded, nonenveloped DNA virusesFamily. ParvoviridaeGenus. ErythrovirusSpecies. Human parvovirus B19 virus
Double-stranded, nonenveloped DNA virusesFamily. PolyomaviridaeGenus. PolyomavirusSpecies. JC polyomavirus, BK polyomavirusFamily. PapillomaviridaeGenus. PapillomavirusSpecies. Human papillomavirusFamily. AdenoviridaeGenus. MastadenovirusSpecies. Human adenoviruses (species A to G)
Double-stranded, enveloped DNA virusesFamily. PoxviridaeGenus. OrthopoxvirusSpecies. Vaccinia virus, variola virus smallpox virus, cowpox virus, monkeypox virusGenus. MolluscipoxvirusSpecies. Molluscum contagiosum virusGenus. ParapoxvirusSpecies. Orf virusFamily. HepadnaviridaeGenus. OrthohepadnavirusSpecies. Hepatitis B virusFamily. HerpesviridaeGenus. SimplexvirusSpecies. Human herpesvirus 1 (herpes simplex virus type 1; HHV-1), human herpesvirus 2 (herpes simplex virus type 2; HHV-2)Genus. VaricellovirusSpecies. Human herpesvirus 3 (varicella-zoster virus [VZV]; HHV-3)Genus. LymphocryptovirusSpecies. Human herpesvirus 4 (Epstein-Barr virus [EBV]; HHV-4)Genus. CytomegalovirusSpecies. Human herpesvirus 5 (CMV; HHV-5)Genus. RoseolovirusSpecies. Human herpesvirus 6 (roseola virus; HHV-6), human herpesvirus 7 (HHV-7)Genus. RhadinovirusSpecies. Human herpesvirus 8 (HHV-8)
Single-stranded, positive-sense, nonenveloped RNA viruses
Family. PicornaviridaeGenus. EnterovirusSpecies. Enterovirus A (human coxsackievirus A2, human enterovirus 71) Enterovirus B (human coxsackievirus B1, human echovirus), Enterovirus C (human poliovirus 1 to 3, human coxsackievirus A1), Enterovirus D (human enterovirus 68, 70, and 94), Rhinovirus A, B, and C.Genus. AphthovirusSpecies. Foot-and-mouth disease virusGenus. HepatovirusSpecies. Human hepatitis A virus (HHAV)
Family. CaliciviridaeGenus. NorovirusSpecies. Norwalk virusGenus. SapovirusSpecies. Sapporo virus
Family. AstroviridaeGenus. AstrovirusSpecies. Human astrovirus
Single-stranded, positive-sense, enveloped RNA viruses
Family. CoronaviridaeGenus. CoronavirusSpecies. Human coronavirus, Severe acute respiratory syndrome (SARS) virus, Middle eastern respiratory syndrome (MERS) virusGenus. TorovirusSpecies. Human torovirus
Family. TogaviridaeGenus. AlphavirusSpecies. Sindbis virus, Eastern equine encephalitis (EEE) virus, Western equine encephalitis (WEE) virus, Venezuelan equine encephalitis (VEE) virus, Chickungunya virus, many other virusesGenus. RubivirusSpecies. Rubella virus
Family. FlaviviridaeGenus. FlavivirusSpecies. Yellow fever virus, West Nile virus, St. Louis encephalitis (SLE) virus, Japanese encephalitis (JE) virus, Dengue virus (types 1 through 4), Zika virus, many other virusesGenus. HepacivirusSpecies. Hepatitis C virus (HCV)
Single-stranded, negative-sense, enveloped RNA viruses
Family. RhabdoviridaeGenus. LyssavirusSpecies. Rabies virus
Family. FiloviridaeGenus. “Marburg-like viruses”Species. Marburg virusGenus. “Ebola-like viruses”Species. Ebola virus
Family. OrthomyxoviridaeGenus. Influenzavirus ASpecies.